I have some thoughts, and questions.
When you set the main speakers to large, did you have the system set up to send bass below 80Hz to both the speakers and the sub, or did you have it set up to only output the LFE to the sub? If you had bass going to both the mains and the sub, then it makes sense that those frequencies would get louder because they are being played at full volume through both the mains and the sub. If, however, you only had bass going to the mains (with the exception of the LFE track), then I have a couple of thoughts.
First, the bass in the frequencies that mattered in that scenario (the ones that made you feel that it was more powerful and realistic) may be played better through your main speakers. It could be that the speakers are just better than the sub at it, or (more likely to me) it's a function of your room acoustics. Perhaps the sub is in a location that causes certain frequencies to be partially cancelled out, at least in your listening position. When playing my sub in my room, there's a big dip in volume around 100Hz in my listening position...but five feet away in another chair, that dip isn't there but rather occurs around 90Hz.
Just some thoughts.